TB-Profiler result

Run: SRR29385400
Summary

Run ID: SRR29385400

Sample name:

Date: 2025-02-11T11:47:20.846555

Number of reads: 6590842

Percentage reads mapped: 99.67

Median coverage: 110.0

Strain: lineage2.2.1;lineage4

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.95
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.06
lineage2.2 East-Asian (Beijing) RD105;RD207 0.63
lineage4 Euro-American None 0.05
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA c.456dupC Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761155 p.Ser450Leu missense_variant 0.85 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.73 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288785 c.456dupC frameshift_variant 0.77 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.9 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 0.64 ethambutol Uncertain significance Mutation from literature
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.94 ethionamide Not assoc w R - Interim
Rv0565c 657188 p.His95Asp missense_variant 0.57 ethionamide Uncertain significance
hadA 731966 p.Arg13Trp missense_variant 0.5 isoniazid Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776356 p.Leu709Ile missense_variant 0.88 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406276 c.1065G>A synonymous_variant 0.62 streptomycin Not assoc w R - Interim
pyrazinamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
ndh 2101774 p.Ser423Arg missense_variant 0.67 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.82 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170487 c.126T>C synonymous_variant 0.79 pyrazinamide Not assoc w R - Interim
pncA 2289469 c.-228C>G upstream_gene_variant 0.67 pyrazinamide
ald 3086788 c.-32T>C upstream_gene_variant 0.85 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.9 pyrazinamide Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.5 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641137 p.Ala199Thr missense_variant 0.82 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246662 p.Val50Ala missense_variant 0.73 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
ethA 4327005 p.Phe157Leu missense_variant 0.93 ethionamide
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.94 streptomycin Not assoc w R
gid 4408182 c.21G>A synonymous_variant 0.78 streptomycin Not assoc w R - Interim